^^^Middle or end - There is a real change here. Watch the first 00:45 seconds of the special, and compare the height of Kirk walking up to window, and you'll see.
Plus there is a pan over from the end of the new movie at the 2:22 mark that matches up.

Maybe ILM and the producers listened to the fans criticism and did a slight/small appeasement.

Actually, it looks to me like they intentionally distorted that particular chunk of the model to accommodate a larger bridge window for that specific shot. Probably this is because the flip-side zoom in cinematography looked weird otherwise and they had to fudge things a bit to make it look right. The model itself actually looks very strange leading right up to that zoom in and never looks like that again in any other shot (and the bridge window is also very much out of proportion with the side windows port and starboard).

It's not hard to guess what the problem was: they wanted the camera to eventually zoom in to Kirk standing in the bridge window showing his face as we got closer. With the original proportions of the window, Kirk would be a very tiny ant in that window until right before the camera flew into it; the buildup of "I see a person... I see a person in a gold shirt... it's Kirk" is kind of diluted in that case. The purpose of that shot wasn't so much to Establish the size of the Enterprise so much as establishing Kirk's location on the Enterprise and the Enterprise's location in the scheme of things; accordingly, they fudged the model a bit to make certain things stand out better than others.

It's kind of annoying, but not exactly meaningful. It's still not quite as bad as the fact that you can't see the saucer section from Jean Luc Picard's ready room window.